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De novo discovery of SNPs for genotyping endangered sun parakeets (Aratinga solstitialis) in Guyana

Spitzer, Robert and Norman, Anita and Königsson, Helena and Schiffthaler, Bastian and Spong, Göran (2020). De novo discovery of SNPs for genotyping endangered sun parakeets (Aratinga solstitialis) in Guyana. Conservation Genetics Resources. 12 , 631-641
[Journal article]

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Abstract

Parrots (Psittaciformes) are among the most endangered groups of birds today and remain threatened by habitat loss and exploitation for the live bird trade. Under such conditions, reliable and non-invasive monitoring techniques are crucial for successful conservation measures. In this study, we developed a panel of 86 high quality SNPs for genotyping endangered sun parakeets (Aratinga solstitialis) in Guyana, which form one of the last known breeding populations of this South American species in the wild. Genotyping was tested on different types of samples (blood, feathers, feces, beak and cloacal swabs). While blood performed best, feathers and feces also yielded reliable results and could thus be used as non-invasive sources of DNA for future population monitoring. Discriminant Analysis of Principal Components (DAPC) on genotypes revealed that Guyanese sun parakeets clustered separately from other psittacine species as well as conspecifics from a captive population. A priori known first-order kinships were also adequately detected by the SNP panel. Using a series of experimental contaminations, we found that contamination from other psittacine species and slight contamination ( 10%) from conspecifics did not prevent successful genotyping and recognition of individuals. We show that instances of higher conspecific contamination ( 50%) can be detected through an increased level of heterozygosity that falls outside the distribution of uncontaminated samples.

Authors/Creators:Spitzer, Robert and Norman, Anita and Königsson, Helena and Schiffthaler, Bastian and Spong, Göran
Title:De novo discovery of SNPs for genotyping endangered sun parakeets (Aratinga solstitialis) in Guyana
Year of publishing :2020
Volume:12
Page range:631-641
Number of Pages:11
ISSN:1877-7252
Language:English
Publication Type:Journal article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Ecology
Keywords:SNP, Sun parakeet, Conservation, Relatedness, Non-invasive sampling, Contamination
URN:NBN:urn:nbn:se:slu:epsilon-p-105740
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-105740
Additional ID:
Type of IDID
DOI10.1007/s12686-020-01151-x
Web of Science (WoS)000533022100001
ID Code:17950
Faculty:S - Faculty of Forest Sciences
Department:(S) > Dept. of Wildlife, Fish and Environmental Studies
Deposited By: SLUpub Connector
Deposited On:27 Oct 2020 13:03
Metadata Last Modified:27 Oct 2020 13:11

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